How can I properly orient custom leaves with a Particle System modifier?
You could use Duplifaces. When the sapling addon creates leaves, each rectangular leaf is a single face (hex leaves are two faced).

Create your custom leaf and then make the leaves object a parent of your leaf. In the object properties for leaves turn on Duplifaces.



Now your custom leaf will be duplicated at the location of each original leaf. The object centre of your leaf will be at the centre of the original face and will be rotated to match the rotation of the original single poly leaf. Modifying the original leaf will adjust every leaf to match. The original poly leaves won't render, just your custom leaf.



To speed up the viewport you can add a decimate modifier to the leaves object to reduce the amount of visible leaves.